beast2
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CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
To reproduce: * start with empty beast/2.7 directory * run `packagemanager -add BEASTLabs` * BEAST.app and BEASTLabs will be installed, but BEAST.base is not there. * Furthermore, `packagemanager -add BEAST.base`...
To reproduce, create a `TreeParser` instance with a labeled newick string and set IsLabelledTree="true". Following the [part of initAndValidate() responsible for sorting the labels alphabetically](https://github.com/CompEvol/beast2/blob/cb25234a1dab3c1fc5e511cb02322eefe09dfb2e/src/beast/base/evolution/tree/TreeParser.java#L187), the leaf nodes in `m_nodes[]`...
Hello, I am the Debian maintainer of beast2. When I run InputForAnnotatedConstructorTest, I get error messages like error: reference to assertEquals is ambiguous [...] both method assertEquals(Object,Object) in Assertions and...
I installed beast 2.7.1 on linux, and immediately tried to update to 2.7.2 with packagemanager -useAppDir -updatenow I did manually correct the JAVA_HOME issue: https://github.com/CompEvol/beast2/commit/0f20d26ae2fd0108c005b64542332a576185045a It fails with the message:...
Hello there, I'm trying to run Coalescent Bayesian Skyline analysises with Beast 2.7.2 on Fedora 36, but it bugs with one of my files: `java.lang.NullPointerException: Cannot invoke "beast.base.evolution.tree.Node.getNr()" because ""...
Hi, I'm trying to compile my package and do some testing on a HPC by following the instructions from [Writing A Beast 2.7 Package](https://www.beast2.org/package-development-guide/writing-a-beast-2_7-package) under the "Preparing your package for...
Hello, I'm encountering this error for some files with Beast v2.7.6. I found that there had been a similar issue in Beast 2.0.2: https://groups.google.com/g/beast-users/c/xrvcxeU4wwA ``` At sample 81010000 Likelihood incorrectly...
It seems there is a bug to resume the XML containing monophyletic clade. The XML to replicate the problem is attached. Run the XML first and then run `beast -resume...
Dear all I am trying to run BEAST2 2.6 version and I keep getting this err message. The full log file and xml file is attached. I would really apppreciate...
Hi, I'm posting this issue here, as the documentation on troubleshooting initialization issues requested it, as this may be a bug. I set up my xml file with BEAUTI, but...
